Molecular structure of the cis‐syn photodimer of d(TpT) (cyanoethyl ester)

Abstract

The three‐dimensional structure was determined by x‐ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis‐syn cyclobutane (CB) geometry and the S‐configuration at the chiral phosphorus atom. The crystals of C₂₃H₃₀N₅O₁₂P · 2H₂O belong to the orthorhombic space group P2₁2₁2₁ (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); ϕ: 141° (86°). These represent half‐chairs designated as ⁶H₁ (T[p]) and ₆H⁵ ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a ²T₃ sugar pucker, and gauche⁻ conformation at C4′‐C5′; the [p]T segment is anti, ³T₄, trans. The C5′‐O5′ torsion of the [p]T unit is –124.5°, and the C3′‐O3′ torsion of the T[p] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P‐O3′ and P‐05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.